Phytolith analysis for differentiating between foxtail millet (Setaria italica) and green foxtail (Setaria viridis)

Foxtail millet (Setaria italica) is one of the oldest domesticated cereal crops in Eurasia, but identifying foxtail millets, especially in charred grains, and differentiating it from its wild ancestor, green foxtail (Setaria viridis), in the archaeobotanical remains, is still problematic. Phytolithic analysis provides a meaningful method for identifying this important crop. In this paper, the silicon structure patterns in the glumes, lemmas, and paleas from inflorescence bracts in 16 modern plants of foxtail millet and green foxtail from China and Europe are examined using light microscopy with phase-contrast and a microscopic interferometer. Our research shows that the silicon structure of ΩIII from upper lemmas and paleas in foxtail millet and green foxtail can be correspondingly divided into two groups. The size of ΩIII type phytolith of foxtail millet is bigger than that from green foxtail. Discriminant function analysis reveals that 78.4% of data on foxtail millet and 76.9% of data on green foxtail are correctly classified. This means certain morphotypes of phytoliths are relatively reliable tools for distinguishing foxtail millet from green foxtail. Our results also revealed that the husk phytolith morphologies of foxtail millets from China and Eastern Europe are markedly different from those from Western Europe. Our research gives a meaningful method of separating foxtail millet and green foxtail. The implications of these findings for understanding the history of foxtail millet domestication and cultivation in ancient civilizations are significant.     

Experimental investigation of pathogenic stress on phytolith formation in Cucurbita pepo var. texana (wild gourd)

Silica phytoliths that form in plant tissues are useful to archaeologists because of their diagnostic value and longevity in ancient deposits. Palaeoecology, site formation processes, plant domestication, and other topics are routinely addressed using phytolith assemblages, especially when macrobotanical remains are not well preserved. However, little research has been conducted to document the effects of ecological variables on phytolith formation. Here, we investigate the effects of mosaic virus and bacterial wilt disease on diagnostic scalloped phytoliths in the rind of a wild-type Cucurbita pepo var texana (gourd). We observe a minimal change in phytolith size distribution between control plants and individuals with mosaic virus. However, we observe a notable difference between plants with bacterial wilt disease and control plants, with diseased individuals carrying a greater proportion of large-diameter scalloped phytoliths. This and similar phenomena could potentially confound archaeological interpretations of phytolith assemblages, and we suggest that the effects of this and other ecological variables should be studied in a diverse range of taxa.     

Morphological variations of lobate phytoliths from grasses in China and the south-eastern United States

Abstract. Phytolith analysis of grasses is a useful tool in palaeoenvironmental and archaeobotanical research. Lobate phytolith is one of the most important morphotypes of grass phytoliths. This study describes morphological variations of diagnostic lobate phytoliths and produces a tentative classification scheme based on 250 modern grass species from China and the south‐eastern U.S.A. Eighty‐five grass species were found to contain lobate phytoliths. They are derived mainly from Panicoideae, but also include the Chloridoideae, Oryzoideae and Arundinoideae subfamilies. Twenty‐five lobate morphological types were observed from different subfamilies, genera or tribes of grasses, based on two important parameters: (1) the length of the lobate shank and (2) the shape of the outer margin of the two lobes. The identification of grass tribe or even genus is possible based on the differences in lobate shape parameters or the composition of assemblages. However, not all of the lobate assemblages have a definite relationship with the genera that produce them, because grasses can only produce a limited range of lobate shapes that often overlap from one genus to another. Several C₃ grasses and Chloridoideae subfamily grasses also produce characteristic lobate phytoliths. The variations of lobate morphologies can be related to environmental factors, especially moisture. Typical hygrophytic grasses tend to yield lobate phytoliths with very short shank, whereas typical xerophytic grasses tend to produce lobate phytoliths with a very long shank. The potential link between phytolith morphology, grass taxonomy and environmental conditions opens the possibility that phytolith morphology may be used as a proxy in palaeoclimatic reconstruction.     

Inter- and intraspecific variation in grass phytolith shape and size: a geometric morphometrics perspective

Background and AimsThe relative contributions of inter- and intraspecific variation to phytolith shape and size have only been investigated in a limited number of studies. However, a detailed understanding of phytolith variation patterns among populations or even within a single plant specimen is of key importance for the correct taxonomic identification of grass taxa in fossil samples and for the reconstruction of vegetation and environmental conditions in the past. In this study, we used geometric morphometric analysis for the quantification of different sources of phytolith shape and size variation.MethodsWe used landmark-based geometric morphometric methods for the analysis of phytolith shapes in two extant grass species (Brachypodium pinnatum and B. sylvaticum). For each species, 1200 phytoliths were analysed from 12 leaves originating from six plants growing in three populations. Phytolith shape and size data were subjected to multivariate Procrustes analysis of variance (ANOVA), multivariate regression, principal component analysis and linear discriminant analysis.Key ResultsInterspecific variation largely outweighed intraspecific variation with respect to phytolith shape. Individual phytolith shapes were classified with 83 % accuracy into their respective species. Conversely, variation in phytolith shapes within species but among populations, possibly related to environmental heterogeneity, was comparatively low.ConclusionsOur results imply that phytolith shape relatively closely corresponds to the taxonomic identity of closely related grass species. Moreover, our methodological approach, applied here in phytolith analysis for the first time, enabled the quantification and separation of variation that is not related to species discrimination. Our findings strengthen the role of grass phytoliths in the reconstruction of past vegetation dynamics.     

Distinguishing rice (Oryza sativa Poaceae) from wild Oryza species through Phytolith analysis: Results of preliminary research

Asian rice is an important grain, not only in its homeland but in many areas of the world. Identifying rice in the archaeological record is a challenge, especially in the moist tropics, where organic materials preserve only when charred. Phytolith analysis, the identification of opaline silica bodies, provides an alternative method for identifying this important crop. Results of our research suggest thatOryza contributes phytoliths that are genus-specific, that bulliform characteristics alone do not permit separation of wild and domesticatedOryza in regions where species overlap, and that a number of phytolith types, especially silicified glumes, show promise for separating wild from domesticated forms. With further research it should be possible to identify rice through its phytolith assemblage in archaeological soils in the heartland of its domestication and use.     

安徽禹会村遗址双墩文化时期农业发展的植硅体证据

本文利用植硅体分析方法,对安徽蚌埠禹会村遗址双墩文化时期44份土壤样品开展植物考古研究,重点关注典型农作物植硅体类型及其形态特征,以及敏感型与固定型植硅体组合特征等。结果显示,禹会村遗址大部分样品中皆发现有水稻特征型植硅体,并未发现粟、黍等旱地作物遗存;水稻扇型及双峰型植硅体形态特征分析显示,水稻遗存为驯化程度较高的粳型稻。以上研究结果表明,该遗址双墩文化时期的农业结构延续了顺山集文化时期以来种植粳型稻为主的传统。此外,通过水稻植硅体高密度样品中敏感型与固定型植硅体含量比值为0.7±0.2推测,该遗址水稻栽培环境属于“高地势-雨水供给”或“低地势-雨水供给”类型。本文研究结果为探讨淮河中游地区新石器时代农业发展、水稻栽培与驯化以及人类适应策略等问题提供了重要科学依据。     

Identifying inflorescence phytoliths from selected species of wheat (Triticum monococcum, T. dicoccon, T. dicoccoides, and T. aestivum) and barley (Hordeum vulgare and H. spontaneum) (Gramineae)

Analysis of microfossil silica phytoliths is becoming an increasingly important research tool for taxonomists, archaeobotanists, and paleoecologists. Expanded use of phytolith analysis by researchers is dependent upon development of phytolith systematics. In this study phytoliths produced by the inflorescence bracts from four species of wheat, Triticum monoccocum, T. dicoccon, T. dicoccoides, and T. aestivum, and two species of barley, Hordeum vulgare, and H. spontaneum, were analyzed using computer-assisted image and statistical analysis with the intent to develop taxonomic tools to distinguish among the taxa. A classification key based on significant differences among the mean morphometries of the inflorescence phytoliths produced by each species was created and tested. Discriminant analysis of the morphometries of several morphotypes of phytoliths was also conducted to determine whether this computer-assisted statistical procedure could be used as another method to classify the taxa and to determine which morphotypes have measurements that can best be used in discriminant functions. Test results indicated that, at the genus level, both the classification key and discriminant analysis of certain morphotypes of phytoliths were relatively reliable tools for distinguishing among phytoliths produced in the inflorescence bracts of the taxa considered. For distinguishing among the taxa at the species level, the classification key was most reliable. Of the discriminant analyses tested, that based on all the phytolith morphotypes combined was more reliable than those based on only one morphotype.     

Early Mixed Farming of Millet and Rice 7800 Years Ago in the Middle Yellow River Region,China

The Peiligang Culture (9000-7000 cal. yr BP) in the Middle Yellow River region, North China, has long been considered representative of millet farming. It is still unclear, however, if broomcorn millet or foxtail millet was the first species domesticated during the Peiligang Culture. Furthermore, it is also unknown whether millet was cultivated singly or together with rice at the same period. In this study, phytolith analysis of samples from the Tanghu archaeological site reveals early crop information in the Middle Yellow River region, China. Our results show that broomcorn millet was the early dry farming species in the Peiligang Culture at 7800 cal. yr BP, while rice cultivation took place from 7800 to 4500 cal. yr BP. Our data provide new evidence of broomcorn millet and rice mixed farming at 7800 cal. yr BP in the Middle Yellow River region, which has implications for understanding the domestication process of the two crops, and the formation and continuance of the Ancient Yellow River Civilization.     

Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica)

Foxtail millet (Setaria italica (L.) Beauv) is one of the earliest domesticated grains, which has been cultivated in northern China by 8,700 years before present (YBP) and across Eurasia by 4,000 YBP. Owing to a small genome and diploid nature, foxtail millet is a tractable model crop for studying functional genomics of millets and bioenergy grasses. In this study, we examined nucleotide sequence diversity, geographic structure, and levels of linkage disequilibrium at four nuclear loci (ADH1, G3PDH, IGS1 and TPI1) in representative samples of 311 landrace accessions across its cultivated range. Higher levels of nucleotide sequence and haplotype diversity were observed in samples from China relative to other sampled regions. Genetic assignment analysis classified the accessions into seven clusters based on nucleotide sequence polymorphisms. Intralocus LD decayed rapidly to half the initial value within ~1.2 kb or less.     

Taxonomic assessment of opal phytoliths from grasses of deltaic West Bengal,India

In the present study, taxonomic potential of opal phytoliths was examined in grasses from lower Gangetic delta, West Bengal, India. The study revealed that finer classification of phytoliths can increase the efficacy of opal silica as taxonomic proxy by minimizing the influences of multiplicity and redundancy. We isolated 187 phytolith sub‐morphotypes, categorized under 10 major groups, from 110 grass species belonging to 45 genera, 21 sub‐tribes, 13 tribes and 7 subfamilies. Cluster and correspondence analyses showed that all the significantly represented subfamilies can be clearly distinguished on the basis of either principal morphotypes or sub‐morphotypes. However, genus/species level discrimination may only be possible by deploying phytolith based identification key developed by utilizing detailed grass phytolith micro‐morphometry and frequency attributes. We conclude that grass phytolith characteristics provide useful and significant information for distinguishing grass taxa of deltaic West Bengal.     

A wet and dry story: distinguishing rice and millet arable systems using phytoliths

Changing rice and millet arable systems were closely linked to social and environmental changes in Neolithic and Early Bronze Age in Central China. Two methods are used here to distinguish between rainfed millet farming and rice farming, using phytoliths from crop weeds found in ash middens and mixed cultural layer contexts. Samples were taken from three sites, Xipo and Huizui, in the Yellow River Valley in Henan, and Baligang which is situated towards the south of the province. The samples are from three cultural phases, Yangshao, Longshan and Erlitou. The phytoliths used are from grass leaves, so are not identified to genera or species but rather grouped into ecological categories, and canonical correspondence analysis was applied. Next, the ratios were calculated of phytolith morphotypes from cells that are genetically predisposed to form phytoliths (fixed), compared to silica bodies from cells that will form silica bodies when there is sufficient water uptake (sensitive). The results show differentiation between millet and rice and differences in how wet the rice fields were. The region experienced social and climate change throughout this time and this is reflected in the results.     

抗拿捕净晋谷21突变体的筛选和分子鉴定

谷子(Setaria italica(L.)P.Beauv.)是我国重要的杂粮作物,具有抗旱耐贫瘠、水分利用率高、适应性广、营养丰富等特点,但谷子田间除草一直制约着谷子的集约化栽培和有机旱作产业规模化的推广与发展.为快速选育抗除草剂谷子品种,本试验以晋谷21突变体M2群体为试验材料,通过喷施0.33％拿捕净除草剂对晋谷...     

内蒙古典型草原禾本科植硅体形态

运用地层中植硅体组合解释过去草原植被及气候变化的关键之一,是要了解研究区现代植硅体形态及表土植硅体组合与现代植被的关系。文中研究内蒙古典型草原禾本科植物根、茎、叶、芒以及种子等不同部位的植硅体,对其中的12种主要禾本科植物叶表皮短细胞硅酸体进行分类及统计。研究表明：内蒙古典型草原禾本科叶表皮短细胞硅酸体可分为8种特殊形态类型。C3植物早熟禾亚科的叶表皮短细胞硅酸体形态多样。几乎所有早熟禾亚科都能产生圆型硅酸体,以贝加尔针茅(85．5％)、大针茅(89．7％)、克氏针茅(90％)以及芨芨草(96．6％)中的圆型硅酸体含量最丰富。针茅哑铃型主要见于针茅植物叶表皮短细胞中,克氏针茅的针茅哑铃型含量相对较高。羊草中未见针茅哑铃型硅酸体。浴草、披缄草叶表皮短细胞硅酸体以齿型为主,分别含87．3％和57．2％,齿型在硬质早熟禾中也占一定比例。沙生冰草中的脊圆型占优势,含74．4％。C3植物早熟禾亚科的叶表皮短细胞产生的截锥型硅酸体含量较少。C4植物虎尾草亚科中的糙隐子草叶表皮短细胞硅酸体以黍哑铃型、简单哑铃型、鞍型为主;黍亚科狗尾草则以黍哑铃型占优势(82．9％)。     

Diversity of lobate phytoliths in grass leaves from the Sahel region, West Tropical Africa: Tribe Paniceae

Phytoliths are microscopic amorphous silicon dioxide (SiO2.H2O) particles occurring in leaves, internodes, glumes and inflorescence within all members of the grass family Poaceae. Phytoliths of grasses are of particular interest, as they possess morphological features which have encouraged many investigators to identify these plants from which fossil phytoliths might have originated. The present study is a step towards preparing a systematic inventory of grass phytoliths in western tropical Africa. Morphology and dimensions of phytoliths from 66 species belonging to the tribe Paniceae have been studied. Four shape categories of lobate phytoliths have been determined in leaf blade spodograms: bilobate, nodular bilobate, polylobate, quadra-lobate. Bilobate shaped phytoliths are frequently represented in all genera of Paniceae. 13 groups of lobate phytoliths have been distinguished based on significant morphological criteria like shape of outer margins, shape of the shank and number of lobes. A size category system of lobate phytolith dimensions (length, width; length and width of shanks) has been developed by the analysis of average, minimum and maximum values of these dimensions. Application of the size category system results on classifying the major groups into 25 subgroups. The study proves that size and shape can be used to assign some of the lobate phytoliths to their respective genera. Some rarely produced lobate shapes like nodular bilobate and polylobate types could be used together on assemblage basis as markers for definite genera in the tribe Paniceae, e.g. Brachiaria, Panicum, Pennisetum and Setaria. Also, bilobate phytoliths with concave margins have been recorded in five species. Bilobate phytoliths with flattened and convex margins and quadra-lobate shapes are produced by almost all species which therefore resulted in an inconsistent and indefinite relationship with the taxa that produce them. The study shows a correlation between width dimensions of bilobate shapes and their shanks. Greater width dimensions usually connected to thick shanks while short ones are attached to thin shanks. A spectrum on percentages of species producing each type of lobate phytolith has been designed. It is recommended that such spectrum should be carried out for all tribes of Poaceae on phyto-geographical basis which might eliminate the effect of redundancy and multiplicity on the classification of grass phytoliths.     

Phytolith assemblages in grasses native to central Argentina

BACKGROUND AND AIMS: Phytolith reference collections are a prerequisite for accurate interpretation of soil phytolith assemblages aimed at reconstructing past vegetation. In this study a phytolith reference collection has been developed for several grasses native to central Argentina: Poa ligularis, Piptochaetium napostaense, Stipa clarazii, Stipa tenuis, Stipa tenuissima, Stipa eriostachya, Stipa ambigua, Stipa brachychaeta, Pappophorum subbulbosum, Digitaria californica, Bothriochloa edwardsiana and Aristida subulata. METHODS: For each species, phytoliths present in the leaf blades were classified into 47 morphotypes, and their relative frequency determined by observing 300-400 phytoliths per sample (n = 5). Data were analyzed by complete linkage cluster analysis, using the Morisita Index as measure of association. KEY RESULTS: The results showed differentiation among phytolith assemblages at species level or at plant functional type level. Cluster analysis separated C3 from C4 species and palatable from non-palatable species. CONCLUSIONS: This study highlights the possibility of reconstructing past vegetation in central Argentina grasslands through the analysis of soil phytolith assemblages.     

A reconstruction of the history of a Holocene sand dune on Great Barrier Island, northern New Zealand, using pollen and phytolith analyses

Aim   To reconstruct the history of a Holocene sand dune using pollen and phytolith analyses, and to identify the strengths, weaknesses and compatibility of these two methods in the interpretation of Quaternary coastal environments.
Location  Great Barrier Island, northern New Zealand.
Methods  Pollen and phytolith analyses were carried out on a sequence through a Holocene sand dune containing a palaeosol.
Results  Phytoliths were present throughout the sequence. Grass phytoliths increased at the expense of tree phytoliths following fire disturbance. Pollen (and spores) was preserved only in the palaeosol part of the profile. Pteridium fern spores increased at the expense of tall tree pollen following the fire disturbance.
Main conclusions  Lack of phytolith production by many species and problems of taxonomic specificity in many others restricts the usefulness of phytolith analysis to defining only broad vegetation types. In New Zealand, gymnosperms are invisible in the phytolith record and ferns are extremely under-represented. In contrast, pollen analysis usually provides a great deal of information regarding the composition of a particular vegetation type. The loss of microscopic charcoal fragments during the phytolith extraction process is a disadvantage in the reconstruction of environments where fires have occurred. The greater durability of phytoliths compared with pollen means that phytoliths may be found in sediments where pollen has not been preserved. The phytolith record may also provide evidence of wetter environments that are not apparent in the pollen record. Unlike grass pollen, which is widely dispersed and therefore blurs the spatial record, the presence of grass phytoliths in sediments indicates a local source. The simultaneous application of both methods potentially provides a powerful tool in ecological interpretation and the reconstruction of Quaternary coastal environments.     

Teosinte inflorescence phytolith assemblages mirror Zea taxonomy

Molecular DNA analyses of the New World grass (Poaceae) genus Zea, comprising five species, has resolved taxonomic issues including the most likely teosinte progenitor (Zea mays ssp. parviglumis) of maize (Zea mays ssp. mays). However, archaeologically, little is known about the use of teosinte by humans both prior to and after the domestication of maize. One potential line of evidence to explore these relationships is opaline phytoliths produced in teosinte fruit cases. Here we use multidimensional scaling and multiple discriminant analyses to determine if rondel phytolith assemblages from teosinte fruitcases reflect teosinte taxonomy. Our results indicate that rondel phytolith assemblages from the various taxa, including subspecies, can be statistically discriminated. This indicates that it will be possible to investigate the archaeological histories of teosinte use pending the recovery of appropriate samples.     

Foxtail millet: a model crop for genetic and genomic studies in bioenergy grasses

Foxtail millet is one of the oldest domesticated diploid C₄ Panicoid crops having a comparatively small genome size of approximately 515?Mb, short life cycle, and inbreeding nature. Its two species, Setaria italica (domesticated) and Setaria viridis (wild progenitor), have characteristics that classify them as excellent model systems to examine several aspects of architectural, evolutionary, and physiological importance in Panicoid grasses especially the biofuel crops such as switchgrass and napiergrass. Foxtail millet is a staple crop used extensively for food and fodder in parts of Asia and Africa. In its long history of cultivation, it has been adapted to arid and semi-arid areas of Asia, North Africa, South and North America. Foxtail millet has one of the largest collections of cultivated as well as wild-type germplasm rich with phenotypic variations and hence provides prospects for association mapping and allele-mining of elite and novel variants to be incorporated in crop improvement programs. Most of the foxtail millet accessions can be primarily abiotic stress tolerant particularly to drought and salinity, and therefore exploiting these agronomic traits can enhance its efficacy in marker-aided breeding as well as in genetic engineering for abiotic stress tolerance. In addition, the release of draft genome sequence of foxtail millet would be useful to the researchers worldwide in not only discerning the molecular basis of biomass production in biofuel crops and the methods to improve it, but also for the introgression of beneficial agronomically important characteristics in foxtail millet as well as in related Panicoid bioenergy grasses.